I need to know about peptide designing and how it is done.
I need to know how to add/ delete or replace amino acids from the protein structure. Which software can help me in doing this?
If you have a PDB file you can use COOT to mutate residues and real space refine. You can also download the electron density from the ESD through the COOT extensions. I suggest after mutating the residues to model the rotamer as closely as the experimentally determined structure (if there is an experimentally determined structure).
http://www.ccp4.ac.uk/index.php
for structure prediction: http://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD/
for modifications:
1. Avogadro: http://avogadro.cc/wiki/Main_Page
2. VMD: http://www.ks.uiuc.edu/Training/Tutorials/vmd-molefacture/tutorial-Molefacture.pdf
I recommend chapter 15 (Stan Tsai : An Introduction to Computational Biochemistry) as a must read to learn about mutating, energy minimization and clash resolving.. etc..
as for structure prediction, I suggest SWISS-MODEL..
Most important is you have to have a hypothesis or a biological meaning of the modeling, otherwise you just end up with unpublishable data.. e.g. what this mutation will do to the protein and how it affects structure or function..
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